1). Yes 2) Right, pull the scale outside of the sqrt() dougOn 02/13/2013 03:36 PM, Clark Fisher wrote: > Hi Doug, > > Thanks for the help, that seemed to worked great. I have a few > follow up questions about how to process the resulting statistics. > > I'm still using v4.5 (can't switch to v5 yet), as I mentioned, and > would like to get the % signal change for certain contrasts with error > bars. Looking through the listserv, I see that the values in > cespct.nii require correction by a scale factor in this version of > fsfast. The most recent conversation I could find on this comes from > 2010, when you told Thomas Janssens: >> Hi Thomas, you may have found a bug in my scale factor calculation. Can >> you compute the new scale factor as described below? BTW, these issues >> are fixed in version 5. >> >> cd bold/analysis >> x = load('X'); >> tirf = x.flac0.ev(3).tirf; >> Xirf = x.flac0.ev(3).Xirf; >> scalefOld = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)])); >> TR = x.flac0.TR; >> dt = tirf(2)-tirf(1); >> scalefNew = sum(Xirf)*TR/dt; > I can't find a follow up to this message. 2 questions. > 1) The results with scalefNew look reasonable to me; do you still think that > this is the proper way to adjust cespct.nii in v4.5? > 2) If I want to put error bars on my % signal change, how do I scale the > values in cesvarpct.nii? I would guess that if I wanted to put a 95% CI on > my % signal change, it would be: > (cespct * scalefNew) +/- ( sqrt(cesvarpct) * scalefNew * 1.96) and NOT > (cespct * scalefNew) +/- ( sqrt(cesvarpct * scalefNew) * 1.96) > Does this sound right, or am I misinterpreting what cesvarpct.nii contains? > Thanks again, > Clark > >> Hi Clark, >> >> On 02/06/2013 05:55 PM, Clark Fisher wrote: >> > Hi everyone, >> > >> > In a previous discussion on this list >> > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg17681.html), >> > Pablo Polosecki was asking the best way to perform hypothesis testing >> > using functional data within an ROI. The final opinion was that it >> > was best to average all of the time courses in the ROI, and re-run the >> > analysis from scratch, so that all of the appropriate whitening, etc. >> > occurred. >> > >> > I was considering doing this, creating a small volume (say, 10 voxels >> > total) that had each voxel holding the average time course from one of >> > 10 ROIs. I would then set up and run a usual fsfast analysis using >> > these tiny volumes. I am using freesurfer 4.5. I have a few questions. >> > >> > 1) Is this reasonable? >> In general, it is reasonable. Though I'm curious what you are ultimately >> trying to do. Do you want p-values for each subject in each ROI? Or will >> you be combining the ROI beta values across subject in a group analysis? >> If so, then the whitening will probably make little, if any, difference, >> especially if this is a blocked design. In expectation, the whitening >> does not affect the beta values. >> > >> > 2) One area where I expect to run into problems is with the whitening. >> > If I set -acfbins to the total number of my dummy voxels, and >> > -acffwhm to 0, will this use the autocorrelation function of the >> > average timecourse within each individual ROI? Is that an appropriate >> > approach? How sensitive will this be to the number of actual voxels >> > averaged to get each ROI (for instance, would this bias me to finding >> > more significant results in ROIs containing fewer voxels?). >> That might work, but no promises! It is an appropriate approach. It >> might be sensitive to the number of voxels if the number is small (say, >> less than 100). >> > >> > 3) Are there other steps that depend upon the spatial arrangement of >> > voxels that I am forgetting, and will these steps choke on these small >> > volumes (or worse, fail in silent but pernicious ways). >> Nothing I can think of off the top of my head. >> doug >> > >> > Thanks for all of the help, >> > Clark >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> >Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop:www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing:ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer